[2024-01-25 17:49:50,969] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b1242b9-e185-4e46-9acf-71eb3400db58/dqc_reference
[2024-01-25 17:49:52,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:52,152] [INFO] Task started: Prodigal
[2024-01-25 17:49:52,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d9a1ecf-adc4-49ff-a591-3332f5b5bf7f/GCF_014836405.1_ASM1483640v1_genomic.fna.gz | prodigal -d GCF_014836405.1_ASM1483640v1_genomic.fna/cds.fna -a GCF_014836405.1_ASM1483640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:59,020] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:59,021] [INFO] Task started: HMMsearch
[2024-01-25 17:49:59,021] [INFO] Running command: hmmsearch --tblout GCF_014836405.1_ASM1483640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b1242b9-e185-4e46-9acf-71eb3400db58/dqc_reference/reference_markers.hmm GCF_014836405.1_ASM1483640v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:59,235] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:59,236] [INFO] Found 6/6 markers.
[2024-01-25 17:49:59,262] [INFO] Query marker FASTA was written to GCF_014836405.1_ASM1483640v1_genomic.fna/markers.fasta
[2024-01-25 17:49:59,262] [INFO] Task started: Blastn
[2024-01-25 17:49:59,262] [INFO] Running command: blastn -query GCF_014836405.1_ASM1483640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b1242b9-e185-4e46-9acf-71eb3400db58/dqc_reference/reference_markers.fasta -out GCF_014836405.1_ASM1483640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:00,074] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:00,076] [INFO] Selected 11 target genomes.
[2024-01-25 17:50:00,076] [INFO] Target genome list was writen to GCF_014836405.1_ASM1483640v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:00,104] [INFO] Task started: fastANI
[2024-01-25 17:50:00,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d9a1ecf-adc4-49ff-a591-3332f5b5bf7f/GCF_014836405.1_ASM1483640v1_genomic.fna.gz --refList GCF_014836405.1_ASM1483640v1_genomic.fna/target_genomes.txt --output GCF_014836405.1_ASM1483640v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:08,922] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:08,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b1242b9-e185-4e46-9acf-71eb3400db58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:08,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b1242b9-e185-4e46-9acf-71eb3400db58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:08,930] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:50:08,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:08,930] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	100.0	953	953	95	conclusive
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	92.132	826	953	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	89.9595	779	953	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	89.8596	768	953	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	86.0008	734	953	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	85.6361	728	953	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.9611	617	953	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	82.4455	634	953	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	80.0926	509	953	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.0745	501	953	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.7616	412	953	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:08,931] [INFO] DFAST Taxonomy check result was written to GCF_014836405.1_ASM1483640v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:08,932] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:08,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:08,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b1242b9-e185-4e46-9acf-71eb3400db58/dqc_reference/checkm_data
[2024-01-25 17:50:08,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:08,962] [INFO] Task started: CheckM
[2024-01-25 17:50:08,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836405.1_ASM1483640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836405.1_ASM1483640v1_genomic.fna/checkm_input GCF_014836405.1_ASM1483640v1_genomic.fna/checkm_result
[2024-01-25 17:50:32,230] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:32,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:32,250] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:32,250] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:32,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836405.1_ASM1483640v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:32,251] [INFO] Task started: Blastn
[2024-01-25 17:50:32,251] [INFO] Running command: blastn -query GCF_014836405.1_ASM1483640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b1242b9-e185-4e46-9acf-71eb3400db58/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836405.1_ASM1483640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:33,608] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:33,610] [INFO] Selected 10 target genomes.
[2024-01-25 17:50:33,611] [INFO] Target genome list was writen to GCF_014836405.1_ASM1483640v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:33,623] [INFO] Task started: fastANI
[2024-01-25 17:50:33,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d9a1ecf-adc4-49ff-a591-3332f5b5bf7f/GCF_014836405.1_ASM1483640v1_genomic.fna.gz --refList GCF_014836405.1_ASM1483640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836405.1_ASM1483640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:41,766] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:41,773] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:41,774] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014836405.1	s__Brevundimonas sp014836405	100.0	953	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000635915.2	s__Brevundimonas naejangsanensis_A	92.5959	800	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.68	97.40	0.91	0.88	5	-
GCF_000421705.1	s__Brevundimonas naejangsanensis	92.132	826	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.43	97.43	0.89	0.89	2	-
GCA_000318405.1	s__Brevundimonas diminuta_B	91.7329	775	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.76	96.50	0.85	0.82	10	-
GCF_003938605.1	s__Brevundimonas sp003938605	90.1564	759	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.78	96.68	0.85	0.83	3	-
GCA_002386585.1	s__Brevundimonas sp002386585	89.9068	632	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.28	96.28	0.79	0.79	2	-
GCF_900163625.1	s__Brevundimonas diminuta_A	89.726	732	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430835.1	s__Brevundimonas sp002430835	89.6234	674	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.55	99.55	0.86	0.86	2	-
GCA_017308115.1	s__Brevundimonas sp017308115	89.5093	693	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	89.2161	768	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:41,776] [INFO] GTDB search result was written to GCF_014836405.1_ASM1483640v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:41,777] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:41,779] [INFO] DFAST_QC result json was written to GCF_014836405.1_ASM1483640v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:41,780] [INFO] DFAST_QC completed!
[2024-01-25 17:50:41,780] [INFO] Total running time: 0h0m51s